SoroushVahidi/scidocs huggingface dataset:
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes
(2015)

DisGeNET is a comprehensive discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET contains over 380,000 associations between >16,000 genes and 13,000 diseases, which makes it one of the largest repositories currently available of its kind. DisGeNET integrates expert-curated databases with text-mined data, covers information on Mendelian and complex diseases, and includes data from animal disease models. It features a score based on the supporting evidence to prioritize gene-disease associations. It is an open access resource available through a web interface, a Cytoscape plugin and as a Semantic Web resource. The web interface supports user-friendly data exploration and navigation. DisGeNET data can also be analysed via the DisGeNET Cytoscape plugin, and enriched with the annotations of other plugins of this popular network analysis software suite. Finally, the information contained in DisGeNET can be expanded and complemented using Semantic Web technologies and linked to a variety of resources already present in the Linked Data cloud. Hence, DisGeNET offers one of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic origin, designed to fulfill the needs of different user profiles, including bioinformaticians, biologists and health-care practitioners. Database URL: http://www.disgenet.org/
A visual tool for ontology alignment to enable geospatial interoperability
(2007)

In distributed geospatial applications with heterogeneous databases, an ontology-driven approach to data integration relies on the alignment of the concepts of a global ontology that describe the domain, with the concepts of the ontologies that describe the data in the distributed databases. Once the alignment between the global ontology and each distributed ontology is established, agreements that encode a variety of mappings between concepts are derived. In this way, users can potentially query hundreds of geospatial databases using a single query. Using our approach, querying can be easily extended to new data sources and, therefore, to new regions. In this paper, we describe the AgreementMaker, a tool that displays the ontologies, supports several mapping layers visually, presents automatically generated mappings, and finally produces the agreements. r 2007 Elsevier Ltd. All rights reserved.
How to Prove Yourself: Practical Solutions to Identification and Signature Problems
(1986)

In this paper we describe simple identification and signature schemes which enable any user to prove his identity and the authenticity of his messages to any other user without shared or public keys. The schemes are provably secure against any known or chosen message attack if factoring is difficult, and typical implementations require only 1% to 4% of the number of modular multiplications required by the RSA scheme. Due to their simplicity, security and speed, these schemes are ideally suited for microprocessor-based devices such as smart cards, personal computers, and remote control systems.
Compact E-Cash
(2005)

This paper presents efficient off-line anonymous e-cash schemes where a user can withdraw a wallet containing 2 coins each of which she can spend unlinkably. Our first result is a scheme, secure under the strong RSA and the y-DDHI assumptions, where the complexity of the withdrawal and spend operations is O( + k) and the user’s wallet can be stored using O( +k) bits, where k is a security parameter. The best previously known schemes require at least one of these complexities to be O(2 · k). In fact, compared to previous e-cash schemes, our whole wallet of 2 coins has about the same size as one coin in these schemes. Our scheme also offers exculpability of users, that is, the bank can prove to third parties that a user has double-spent. We then extend our scheme to our second result, the first e-cash scheme that provides traceable coins without a trusted third party. That is, once a user has double spent one of the 2 coins in her wallet, all her spendings of these coins can be traced. However, the price for this is that the complexity of the spending and of the withdrawal protocols becomes O( · k) and O( · k + k) bits, respectively, and wallets take O( · k) bits of storage. All our schemes are secure in the random oracle model.
Chain : Operator Scheduling for Memory Minimization in Data Stream Systems
(2003)

In many applications involving continuous data streams, data arrival is bursty and data rate fluctuates over time. Systems that seek to give rapid or real-time query responses in such an environment must be prepared to deal gracefully with bursts in data arrival without compromising system performance. We discuss one strategy for processing bursty streams --- adaptive, load-aware scheduling of query operators to minimize resource consumption during times of peak load. We show that the choice of an operator scheduling strategy can have significant impact on the run-time system memory usage. We then present Chain scheduling, an operator scheduling strategy for data stream systems that is near-optimal in minimizing run-time memory usage for any collection of single-stream queries involving selections, projections, and foreign-key joins with stored relations. Chain scheduling also performs well for queries with sliding-window joins over multiple streams, and multiple queries of the above types. A thorough experimental evaluation is provided where we demonstrate the potential benefits of Chain scheduling, compare it with competing scheduling strategies, and validate our analytical conclusions.
LaBB-CAT: an Annotation Store
(2012)

“ONZE Miner”, an open-source tool for storing and automatically annotating Transcriber transcripts, has been redeveloped to use “annotation graphs” as its data model. The annotation graph framework provides the new software, “LaBB-CAT”, greater flexibility for automatic and manual annotation of corpus data at various independent levels of granularity, and allows more sophisticated annotation structures, opening up new possibilities for corpus mining and conversion between tool formats.
Agile in Public Administration: Oxymoron or Reality? An Experience Report
(2013)

In the last 10 years, Agile methods and practices have emerged as an alternative for software development. Different "flavors" of Agile have appeared ranging from project management to tests organization. These approaches have being gaining popularity and involve now a solid option for organizations developing software, but what about Public Administrations? Is Agile a suitable option for developing software in Public Administrations? Even if Public Administrations have been traditionally regarded as changeresistant, Agile approach can also provide them with the benefits of quick adaptation and frequent value delivery. This paper presents the results of two different projects, which use an Agile framework based on Scrum, developed by a Spanish Public Administration. Additionally, after considering the obtained results, it takes out some relevant learned lessons on the suitability of applying Agile approaches to Public Administration environments.
Machine Health Monitoring Using Local Feature-Based Gated Recurrent Unit Networks
(2018)

In modern industries, machine health monitoring systems (MHMS) have been applied wildly with the goal of realizing predictive maintenance including failures tracking, downtime reduction, and assets preservation. In the era of big machinery data, data-driven MHMS have achieved remarkable results in the detection of faults after the occurrence of certain failures (diagnosis) and prediction of the future working conditions and the remaining useful life (prognosis). The numerical representation for raw sensory data is the key stone for various successful MHMS. Conventional methods are the labor-extensive as they usually depend on handcrafted features, which require expert knowledge. Inspired by the success of deep learning methods that redefine representation learning from raw data, we propose local feature-based gated recurrent unit (LFGRU) networks. It is a hybrid approach that combines handcrafted feature design with automatic feature learning for machine health monitoring. First, features from windows of input time series are extracted. Then, an enhanced bidirectional GRU network is designed and applied on the generated sequence of local features to learn the representation. A supervised learning layer is finally trained to predict machine condition. Experiments on three machine health monitoring tasks: tool wear prediction, gearbox fault diagnosis, and incipient bearing fault detection verify the effectiveness and generalization of the proposed LFGRU.
Sparse Probabilistic Principal Component Analysis
(2009)

Principal component analysis (PCA) is a popular dimensionality reduction algorithm. However, it is not easy to interpret which of the original features are important based on the principal components. Recent methods improve interpretability by sparsifying PCA through adding an L1 regularizer. In this paper, we introduce a probabilistic formulation for sparse PCA. By presenting sparse PCA as a probabilistic Bayesian formulation, we gain the benefit of automatic model selection. We examine three different priors for achieving sparsification: (1) a two-level hierarchical prior equivalent to a Laplacian distribution and consequently to an L1 regularization, (2) an inverse-Gaussian prior, and (3) a Jeffrey’s prior. We learn these models by applying variational inference. Our experiments verify that indeed our sparse probabilistic model results in a sparse PCA solution.
Template-Free Construction of Poems with Thematic Cohesion and Enjambment
(2017)

Existing poetry generation systems usually focus on particular features of poetry (such as rhythm, rhyme, metaphor) and specific techniques to achieve them. They often resort to template-base solutions, in which it is not always clear how many of the alleged features of the outputs were already present in the template employed. The present paper considers two specific features – thematic consistency, and enjambment – and presents an ngram based construction method that achieves these features without the use of templates. The construction procedure is not intended to produce poetry of high quality, only to achieve the features considered specifically in its design. A set of metrics is defined to capture these features in quantitative terms, and the metrics are applied to system outputs and to samples of both human and computer generated poetry. The results of these tests are discussed in terms of the danger of to ignoring certain features when designing construction procedures but valuing them during evaluation even if they arise from hard-wiring in the resources or serendipitous emergence, and the fundamental need for poets to develop a personal voice – fundamental for human poets and inconsistent with the application of Turing tests.
MovieGEN : A Movie Recommendation System
(2008)

In this paper we introduce MovieGEN, an expert system for movie recommendation. We implement the system using machine learning and cluster analysis based on a hybrid recommendation approach. The system takes in the users’ personal information and predicts their movie preferences using well-trained support vector machine (SVM) models. Based on the SVM prediction it selects movies from the dataset, clusters the movies and generates questions to the users. Based on the users’ answers, it refines its movie set and it finally recommends movies for the users. In the process we traverse the parameter space, thus enabling the customizability of the system.
A harmonic suppression circularly polarized patch antenna for an RF ambient energy harvesting system
(2013)

This paper presented a new design of harmonic suppression microstrip patch antenna with the circular polarization properties at frequency 900MHz for an RF ambient energy harvesting system. The purpose of harmonic suppression antenna is to eliminate the using of a harmonic filter circuit in filtering the unwanted signal at the harmonic frequencies in a rectenna system. By introducing a truncating to corner of the rectangular microstrip patch antenna to achieved the required axial ratio, an antenna with circular polarization property is presented. The dimension of patch is reduced by applying partially ground plane. Then an implementation of a defected ground structure (DGS) with a circular shape slot, the unwanted radiation at harmonic frequencies are successfully suppressed. The patch antenna is designed on an FR4 substrate with εr=4.7 and a thickness of 1.6 mm has -20dB return loss at 900 MHz and suppress the second and third harmonic up to -2dB. The proposed circularly polarized harmonic suppression antenna is then fabricated and measured for the verification of the design.
Conceptualizing and testing formative constructs: tutorial and annotated example
(2009)

Although abundant advice is available for how to develop and validate multi-item scales based on reflective constructs, scant attention has been directed to how to construct and validate formative constructs. Such advice is important because (1) theory suggests many constructs are formative and (2) recent advances in software render testing models with formative constructs more tractable. In this tutorial, our goal is to enhance understanding of formative constructs at the conceptual, statistical and methodological levels. Specifically, we (1) provide general principles for specifying whether a construct should be conceptually modeled as reflective or formative, (2) discuss the statistical logic behind formative constructs, and (3) illustrate how to model and evaluate formative constructs. In particular, we provide a tutorial in which we test and validate professional reward structure, a formative construct, in two popular structural equation modeling programs: EQS and PLS. We conclude with a summary of guidelines for how to conduct and evaluate research using formative constructs.
Exemplar-Based Portrait Style Transfer
(2018)

Transferring the style of an example image to a content image opens the door of artistic creation for end users. However, it is especially challenging for portrait photos since human vision system is sensitive to the slight artifacts on portraits. Previous methods use facial landmarks to densely align the content face with the style face to reduce the artifacts. However, they can only handle the facial region. As for the whole image, building the dense correspondence is difficult and may easily introduce errors. In this paper, we propose a robust approach for portrait style transfer that gets rid of dense correspondence. Our approach is based on the guided image synthesis framework. We propose three novel guidance maps for the synthesis process. Contrary to former methods, these maps do not require the dense correspondence between content image and style image, which allows our method to handle the whole portrait photo instead of facial region only. In comparison with recent neural style transfer methods, our method achieves more pleasing results and preserves more texture details. Extensive experiments demonstrate our advantage over former methods on portrait style transfer.
Tracking football player movement from a single moving camera using particle filters
(2006)

This paper deals with the problem of tracking football players in a football match using data from a single moving camera. Tracking footballers from a single video source is di cult: not only do the football players occlude each other, but they frequently enter and leave the camera's eld of view, making initialisation and destruction of a player's tracking a di cult task. The system presented here uses particle lters to track players. The multiple state estimates used by a particle lter provide an elegant method for maintaining tracking of players following an occlusion. Automated tracking can be achieved by creating and stopping particle lters depending on the input player data.
Compact hashing with joint optimization of search accuracy and time
(2011)

Similarity search, namely, finding approximate nearest neighborhoods, is the core of many large scale machine learning or vision applications. Recently, many research results demonstrate that hashing with compact codes can achieve promising performance for large scale similarity search. However, most of the previous hashing methods with compact codes only model and optimize the search accuracy. Search time, which is an important factor for hashing in practice, is usually not addressed explicitly. In this paper, we develop a new scalable hashing algorithm with joint optimization of search accuracy and search time simultaneously. Our method generates compact hash codes for data of general formats with any similarity function. We evaluate our method using diverse data sets up to 1 million samples (e.g., web images). Our comprehensive results show the proposed method significantly outperforms several state-of-the-art hashing approaches.
Blockchain as a Platform for Secure Inter-Organizational Business Processes
(2018)

Today, most of the services one may think of are based on a collaborative paradigm (e.g., social media services, IoT-based services, etc.). One of the most relevant representative of such class of services are inter-organizational processes, where an organized group of joined activities is carried out by two or more organizations to achieve a common business goal. Inter-organizational processes are therefore vital to achieve business partnerships among different organizations. However, they may also pose serious security and privacy threats to the data each organization exposes. This is mainly due to the weak trust relationships that may hold among the collaborating parties, which result in a potential lack of trust on how data/operations are managed. In this paper, we discuss, how blockchain, one of today hottest technology, can be used in support of secure inter-organizational processes. We further point out which additional security issues the use of blockchain can bring, illustrate the ongoing research projects in the area and discuss future research directions.
Exploiting 2D Floorplan for Building-Scale Panorama RGBD Alignment
(2017)

This paper presents a novel algorithm that utilizes a 2D floorplan to align panorama RGBD scans. While effective panorama RGBD alignment techniques exist, such a system requires extremely dense RGBD image sampling. Our approach can significantly reduce the number of necessary scans with the aid of a floorplan image. We formulate a novel Markov Random Field inference problem as a scan placement over the floorplan, as opposed to the conventional scan-to-scan alignment. The technical contributions lie in multi-modal image correspondence cues (between scans and schematic floorplan) as well as a novel coverage potential avoiding an inherent stacking bias. The proposed approach has been evaluated on five challenging large indoor spaces. To the best of our knowledge, we present the first effective system that utilizes a 2D floorplan image for building-scale 3D pointcloud alignment. The source code and the data are shared with the community to further enhance indoor mapping research.
Impact of singular excessive computer game and television exposure on sleep patterns and memory performance of school-aged children.
(2007)

OBJECTIVE
Television and computer game consumption are a powerful influence in the lives of most children. Previous evidence has supported the notion that media exposure could impair a variety of behavioral characteristics. Excessive television viewing and computer game playing have been associated with many psychiatric symptoms, especially emotional and behavioral symptoms, somatic complaints, attention problems such as hyperactivity, and family interaction problems. Nevertheless, there is insufficient knowledge about the relationship between singular excessive media consumption on sleep patterns and linked implications on children. The aim of this study was to investigate the effects of singular excessive television and computer game consumption on sleep patterns and memory performance of children.


METHODS
Eleven school-aged children were recruited for this polysomnographic study. Children were exposed to voluntary excessive television and computer game consumption. In the subsequent night, polysomnographic measurements were conducted to measure sleep-architecture and sleep-continuity parameters. In addition, a visual and verbal memory test was conducted before media stimulation and after the subsequent sleeping period to determine visuospatial and verbal memory performance.


RESULTS
Only computer game playing resulted in significant reduced amounts of slow-wave sleep as well as significant declines in verbal memory performance. Prolonged sleep-onset latency and more stage 2 sleep were also detected after previous computer game consumption. No effects on rapid eye movement sleep were observed. Television viewing reduced sleep efficiency significantly but did not affect sleep patterns.


CONCLUSIONS
The results suggest that television and computer game exposure affect children's sleep and deteriorate verbal cognitive performance, which supports the hypothesis of the negative influence of media consumption on children's sleep, learning, and memory.
A Nonisolated Three-Port DC–DC Converter and Three-Domain Control Method for PV-Battery Power Systems
(2015)

In order to interface one photovoltaic (PV) port, one bidirectional battery port, and one load port of a PV-battery dc power system, a novel nonisolated three-port dc/dc converter named boost bidirectional buck converter (B3C) and its control method based on three-domain control are proposed in this paper. The power flow and operating principles of the proposed B3C are analyzed in detail, and then, the dc voltage relation between three ports is deduced. The proposed converter features high integration and single-stage power conversion from both PV and battery ports to the load port, thus leading to high efficiency. The current of all three ports is continuous; hence, the electromagnetic noise can be reduced. Furthermore, the control and modulation method for B3C has been proposed for realizing maximum power point tracking (MPPT), battery management, and bus voltage regulation simultaneously. The operation can be transited between conductance mode and MPPT mode automatically according to the load power. Finally, experimental verifications are given to illustrate the feasibility and effectiveness of the proposed topology and control method.
A CRISPR/Cas-Mediated Selection-free Knockin Strategy in Human Embryonic Stem Cells
(2015)

The development of new gene-editing tools, in particular the CRISPR/Cas system, has greatly facilitated site-specific mutagenesis in human embryonic stem cells (hESCs), including the introduction or correction of patient-specific mutations for disease modeling. However, integration of a reporter gene into an endogenous locus in hESCs still requires a lengthy and laborious two-step strategy that involves first drug selection to identify correctly targeted clones and then excision of the drug-resistance cassette. Through the use of iCRISPR, an efficient gene-editing platform we recently developed, this study demonstrates a knockin strategy without drug selection for both active and silent genes in hESCs. Lineage-specific hESC reporter lines are useful for real-time monitoring of cell-fate decisions and lineage tracing, as well as enrichment of specific cell populations during hESC differentiation. Thus, this selection-free knockin strategy is expected to greatly facilitate the use of hESCs for developmental studies, disease modeling, and cell-replacement therapy.